No, Visual Micro does not alter any of the ide program files. Visual Micro only installs its own files under the program files folder. It also adds a few new project templates which are usually located in 'mydocuments/vs_ver/project templates'

Does the Visual Micro installer alter any core Arduino Ide program files?

No, Visual Micro does not alter any of the Ide program files. The Arduino Ide is unchanged and is not used by Visual Micro except to confirm the Arduino Ide is installed and to read the 'configuration files/hardware'
source codes

Does editing my programs with Visual Micro alter any of my core or library sources? Can I still program my code with the Arduino Ide after using Visual Micro?

Visual Micro does not change any source code! The code remains the way it was authored and will work as designed in either Visual Micro or the Arduino Ide

How can I find the version of Visual Micro that is currently installed?

The current version can be found by looking at Tools>Options>Visual Micro>Version. The Service Pack level is also shown below the version number.

Can Visual Studio and Atmel Studio be installed on the same
computer?

Yes, all versions of Visual
Studio and Atmel Studio can coexist on the same computer without causing
any issues.

I have deleted files from my project, but they are still used in compilation

If you have removed a file from your project by pressing
[Del] in the Solution Explorer, you had the choice to remove
it from the project or to delete it from your hard drive. If you choose
only to remove it, it will still be part of the compilation.

Open Windows explorer and delete the file. If you want to keep it but
exclude it from the compilation, simply rename the file extension, e.g.
from "myfile.cpp" to "myfile.__cpp"

After making changes to my project, I get strange compiler errors or
my sketch will not run correctly anymore, but I can’t find any mistakes
in my code. What shall I do?

or

I have manually changed various library and/or core source codes and need
to ensure a clean compilation

Sometimes, in advanced projects, changes to #defines or changes to library
code require a clean build. This page
describes how to perform a clean build.

When I try to create a new sketch or add an
existing sketch, I get the message
"Unable to create an Arduino project for Atmel Studio"

This can occur when using Atmel Studio 6.2.
In this case, uninstall Visual Micro and reinstall it as an administrator by right
clicking on Visual Micro's installer file and choose "Run as
administrator".

When trying to build my sketch, I get the error
message "'xxxx' was not declared in this scope", although
xxxx is declared correctly

This problem may occur if two conditions are met:
1. You have used a C++ typedef as a parameter for a
function definition
2. Your function is in an .INO file

I have problems with foreign
characters like "ä" and "Д", and the original Arduino IDE handled
them differently.

If you have such characters in your code, then
you will notice that they will all be translated into the same three byte code
0xef 0xbf 0xbd in your compiled program.This
article explains how to repair this and gives you general advice
about handling Non-ASCII characters.

I have renamed one of my .INO files and now the
sketch does not compile anymore

This may come from the way how
Visual Micro combines all .INO files into one big INO file.

Debugging

I have enabled debugging but it does not work

Please keep in mind that the debugging system uses the serial port
and expects a baud rate as set in Visual Micro. If your sketch
code uses the serial port as well, then you must use the same baud rate
as Visual Micro (in your Serial.begin() function call) or adjust
Visual Micro's
baud rate to yours.

Visual Micro's default baud rate is 115.200, you can change the baud
rate in the Project
Properties (Local Speed and Remote Speed
settings).

As an alternative, you can use separate serial ports for debugging and
other communications (Read more)

Can I use the debugger to debug interrupt service routines (ISRs)?

yes, at least for certain ISRs this is possible. To make the debugger usable with ISRs, switch off the
"throttle" function in the
project properties.